Careful with acid on the rind. Yes, this does help 'wipe off' the moldy spots, but also it will kill or at least stunt the things we want to have growing. Wine has a mild acid content already. I hesitate to use more acid than this, unless things get seriously out of hand.
But even then, I would't use vinegar. One cheese I had at home got seriously moldy, but I reclaimed it without acid. I scraped off the mold and put it back on a pretty strict washing regiment. Not a spot of the mold ever showed up again (unfortunately it had already put a little flavor in the rind, and left a dark spot that will never go away)
I prefer not to use any commercial cultures for washing -I even have left off of commercial cultures for the make, and have gone over to isolating my own wild cultures. For me, it's something of an art, a craft. I like to get my flavors from the world around me, like my ancestors before me did. That way, I feel like my products are a little more connected to the world from which they come. But not everyone wants to do that. It takes some diligence to get your own wild strains of Linens going, and some amount of knowledge to be able to isolate the ones you want. As for the stuff growing in the home, It's the same stuff you buy anyway...
But also, with all of this comes the fact that my system is geared to the fact that I make cheese every day. The cultures I make are highly perishable -I can keep them stored for very long at all, they aren't freeze dried or anything like that, just liquids full of live, hungry, happy bacteria that need to be used up within a pretty small window (like, a time span of a few hours). SO that means my methods might not be practical for you, unless you are the diligent farmer or farm wife that takes the leftover milk from the family cow and makes a batch several times a week.
Now, about the gruyere make,
I suspect you should have let it coagulate a bit longer. For example:
Our Alpkäse is an extra-hard cheese, and it coagulates with a certain amount of rennet for 30 minutes. Our rennet is quality controlled so that we know the proper amounts to use, we don't use the floc method but as I understand that system, we use a multiplier of 2. Makers of Gruyere using the same amount of rennet would typically coagulate their cheese for around 45 minutes. Other than that, the making process for the 2 cheeses are almost identical. So, that would imply a multiplier for true Swiss Gruyere of about 3.
So taking your floc time of 20 minutes, you should have coagulated for about an hour. (You used slightly less rennet or weaker rennet than would typically be used)
Also, the strength of the curd we go for in the Alps is A LOT thinner than what I see most people aiming for in America on the same cheese. This means that the cheese you get from Switzerland will often be a little bit harder than their American counterparts. I have noticed this to be true, especially with Emmentaler.
Now for brown spots,
If you are talking about what I think, these are natural results of the Linens. As the linens do their thing, they produce pigment. The color change in the rind will often be spotty at first, and in some strains it might never be consistent. Some strains are pink, some are bright orange, some are deep red, some are a sort of burnt orange, and some are golden brown. Mine are the golden brown variety, many commercial cultures will be red or orange.
Unless you have good reason to believe the brown spots are the work of mold or yeast, let them be and let them spread.
Always remember with the Schmier, we want to cheese to eventually change color. And when we get spotty color, it's our job to work up those bugs and spread them around.